Patrick Roelli

Those are definitely trimmed. The numbers appearing are the different lengths of sequences found.

I'm assuming quality trimmed. If I'm not mistake, the bcl2fastq can trim bases based on quality and since this kind of data normally have long polyA stretches after the TAG...

Right now, no. I can fix it up over the weekend though.

Hello @ibseq the latest develop branch should work for you. Can you try it out?

Oh you have to install from source, it's not released yet: `pip install git+https://github.com/Hoohm/CITE-seq-Count/@develop`

You are still using the official release. Those checks are gone in the develop. Can you uninstall all CITE-seq-Count install before installing the develop version. `pip uninstall CITE-seq-Count` `pip uninstall...

My bad, I had two checks in place. Should be gone now

Interesting. How many cores did you provide? On Mon, 4 May 2020 at 09:54, ibseq wrote: > it did run for a while but stopped with this: > > Traceback...

Was there another error? It feels like there was a crach during mapping

Yeah, there is an error: `hamming expected two unicodes of the same length` It's linked to the trimming stuff. I don't have a randomly trimmed dataset on my hands right...